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Abstract The incidence of multiple primary lung cancer (MPLC) is increasing, with some of our surgical patients exhibiting numerous lesions. We defined lung cancer with five or more primary lesions as super MPLCs. Elucidating the genomic characteristics of this special MPLC subtype can help reduce disease burden and understand tumor evolution. In our cohort of synchronous super early-stage MPLCs (PUMCH-ssesMPLC), whole-exome sequencing on 130 resected malignant specimens from 18 patients provided comprehensive super-MPLC genomic landscapes. Mutations are enriched in PI3k-Akt and MAPK pathways. Their BRAF mutation frequency (31.5%) is significantly higher than MPLC with fewer lesions and early-stage single-lesion cancer, while EGFR mutations are significantly fewer (13.8%). As lesion counts increase, BRAF mutations gradually become dominant. Also, invasive lesions more tend to have classic super-MPLC mutation patterns. High-frequency BRAF mutations, especially Class II, and low-frequency EGFR mutations could be a reason for the limited effectiveness of targeted therapy in super-MPLC patients.

ABSTRACT: Aflatoxin B1 (AFB1) is a mycotoxin which is responsible for severe damage to the immune system of humans and livestock. Licochalcone A (Lico A), a polyphenol derived from turmeric, has attracted great attention due to its wonderful antioxidant properties. Ferroptosis, an iron-dependent cell death related to oxidative stress, which plays a crucial role in the resistance of phytochemical to immune-associated injury. Nevertheless, effects of Lico A on the bursa of broilers exposed to AFB1 remain unclear. In this work, broilers were fed diets supplemented with 2 mg/kg of AFB1 and 50 mg/kg of Lico A. Meanwhile, various concentrations of Lico A and AFB1 (15 μM) were used to stimulate macrophages. These results revealed that AFB1 resulted in more severe bursa atrophy and relative weight reduction; the expression of pro-ferroptosis protein ACSL4 and the content of malondialdehyde (MDA) were significantly elevated, while the expression of anti-ferroptosis proteins GPX4, xCT, FSP1 and the content of Glutathione (GSH) was obviously reduced. However, Lico A treatment effectively reversed these effects in the bursa of broilers. Meanwhile, in bursa and macrophages, Lico A mitigated the expression of AFB1-induced apoptosis-associated protein (Caspase-3, Bax, Bcl-2) as well as antioxidant protein (Nrf2, GCLM, HO-1). Importantly, ferroptosis was also observed in macrophages induced by AFB1. Lico A efficaciously alleviated AFB1-induced mitochondrial membrane potential decrease and reactive oxygen species (ROS) production in macrophages; in contrast, Lico A evidently inhibited AFB1-triggered ROS generation and cytotoxicity, which was disabled by the addition of Erastin. Moreover, Liproxstatin-1 significantly inhibited ROS generation induced by AFB1. In summary, the present study elucidates that the main mechanism by which Lico A attenuates AFB1-induced immunotoxicity is through the suppression of ferroptosis, apoptosis, mitochondrial damage and oxidative stress, which is promising for the improvement of immunotoxic effects of AFB1.

Abstract Spatial transcriptomics (ST) assays represent a revolution in how the architecture of tissues is studied by allowing for the exploration of cells in their spatial context. A common element in the analysis is delineating tissue domains or “niches” followed by detecting differentially expressed genes to infer the biological identity of the tissue domains or cell types. However, many studies approach differential expression analysis by using statistical approaches often applied in the analysis of non-spatial scRNA data (e.g., two-sample t-tests, Wilcoxon’s rank sum test), hence neglecting the spatial dependency observed in ST data. In this study, we show that applying linear mixed models with spatial correlation structures using spatial random effects effectively accounts for the spatial autocorrelation and reduces inflation of type-I error rate observed in non-spatial based differential expression testing. We also show that spatial linear models with an exponential correlation structure provide a better fit to the ST data as compared to non-spatial models, particularly for spatially resolved technologies that quantify expression at finer scales (i.e., single-cell resolution).

Abstract Background Breast cancer ranks first among malignant tumors, of which triple-negative breast cancer (TNBC) is characterized by its highly invasive behavior and the worst prognosis. Timely diagnosis and precise treatment of TNBC are substantially challenging. Abnormal tumor vessels play a crucial role in TNBC progression and treatment. Nitric oxide (NO) regulates angiogenesis and maintains vascular homeostasis, while effective NO delivery can normalize the tumor vasculature. Accordingly, we have proposed here a tumor vascular microenvironment remodeling strategy based on NO-induced vessel normalization and extracellular matrix collagen degradation with multimodality imaging-guided nanoparticles against TNBC called DNMF/PLGA. Results Nanoparticles were synthesized using a chemotherapeutic agent doxorubicin (DOX), a NO donor L-arginine (L-Arg), ultrasmall spinel ferrites (MnFe2O4), and a poly (lactic-co-glycolic acid) (PLGA) shell. Nanoparticle distribution in the tumor was accurately monitored in real-time through highly enhanced magnetic resonance imaging and photoacoustic imaging. Near-infrared irradiation of tumor cells revealed that MnFe2O4 catalyzes the production of a large amount of reactive oxygen species (ROS) from H2O2, resulting in a cascade catalysis of L-Arg to trigger NO production in the presence of ROS. In addition, DOX activates niacinamide adenine dinucleotide phosphate oxidase to generate and supply H2O2. The generated NO improves the vascular endothelial cell integrity and pericellular contractility to promote vessel normalization and induces the activation of endogenous matrix metalloproteinases (mainly MMP-1 and MMP-2) so as to promote extravascular collagen degradation, thereby providing an auxiliary mechanism for efficient nanoparticle delivery and DOX penetration. Moreover, the chemotherapeutic effect of DOX and the photothermal effect of MnFe2O4 served as a chemo-hyperthermia synergistic therapy against TNBC. Conclusion The two therapeutic mechanisms, along with an auxiliary mechanism, were perfectly combined to enhance the therapeutic effects. Briefly, multimodality image-guided nanoparticles provide a reliable strategy for the potential application in the fight against TNBC. Graphical Abstract

Abstract RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.

The complexity of diagenesis and hydrocarbon accumulation in the deep reservoirs in southern Junggar Basin restricts hydrocarbon exploration in the lower reservoir assemblage. The lithofacies and diagenesis of reservoirs in the Cretaceous Qingshuihe Formation in the Gaoquan structure of the Sikeshu Sag, southern Junggar Basin were analyzed. On this basis, the thermal history was calibrated using calcite in-situ U-Pb dating and fluid inclusion analysis to depict the hydrocarbon accumulation process in the Gaoquan structure. The results show that the Qingshuihe reservoir experienced two phases of calcite cementation and three phases of hydrocarbon charging. The calcite cements are dated to be 122.1±6.4 Ma, 14.4±1.0 Ma –14.2±0.3 Ma. The hydrocarbon charging events occurred at around 14.2–30.0 Ma (low-mature oil), 14.2 Ma (mature oil), and 2 Ma (high-mature gas). The latter two phases of hydrocarbon charging contributed dominantly to the formation of reservoir. Due to the S-N compressive thrust activity during the late Himalayan period since 2 Ma, the traps in the Gaoquan structure were reshaped, especially the effective traps which developed in the main reservoir-forming period were decreased significantly in scale, resulting in weak hydrocarbon shows in the middle-lower part of the structure. This indicates that the effective traps in key reservoir-forming period controlled hydrocarbon enrichment and distribution in the lower reservoir assemblage. Calcite U-Pb dating combined with fluid inclusion analysis can help effectively describe the complex diagenesis and hydrocarbon accumulation process in the central-west part of the basin.

Abstract Controlling site-selectivity and reactivity in chemical reactions continues to be a key challenge in modern synthetic chemistry. Here, we demonstrate the discovery of site-selective chemical reactions on the water surface via a sequential assembly approach. A negatively charged surfactant monolayer on the water surface guides the electrostatically driven, epitaxial, and aligned assembly of reagent amino-substituted porphyrin molecules, resulting in a well-defined J-aggregated structure. This constrained geometry of the porphyrin molecules prompts the subsequent directional alignment of the perylenetetracarboxylic dianhydride reagent, enabling the selective formation of a one-sided imide bond between porphyrin and reagent. Surface-specific in-situ spectroscopies reveal the underlying mechanism of the dynamic interface that promotes multilayer growth of the site-selective imide product. The site-selective reaction on the water surface is further demonstrated by three reversible and irreversible chemical reactions, such as imide-, imine-, and 1, 3-diazole (imidazole)- bonds involving porphyrin molecules. This unique sequential assembly approach enables site-selective chemical reactions that can bring on-water surface synthesis to the forefront of modern organic chemistry.

Cryptocaryon irritans (C. irritans) is a proto-ciliate parasite that infects marine fishes, including the cultured species Takifugu rubripes (T. rubripes), causing disease and potential mortality. In host organisms, infection by parasites triggers an immune response that is modulated by regulatory elements including proteins and non-coding RNAs. In this study, the whole transcriptome RNA sequencing of T. rubripes gill tissue before and after infection with C. irritans was performed to reveal the competitive endogenous RNA (ceRNA) regulatory network. Histomorphology revealed gill segment swelling and parasitic invasion in the infected group. The analysis identified 18 differentially expressed miRNAs (DEMs), 214 lncRNAs (DELs), 2501 genes (DEGs), and 7 circRNAs (DECs) in the infected group. Gene Ontology (GO) enrichment analysis revealed that these genes were notably enriched in the Wnt signaling pathway and mTOR signaling pathway. The co-expression networks (lncRNA/circRNA-miRNA-mRNA) were constructed based on correlation analysis of the differentially expressed RNAs. Further analysis suggested that the LOC105418663-circ_0000361-fru-miR-204a-fzd3a ceRNA axis was potentially involved in the regulation of immune responses against C. irritans infection. Finally, the expression levels of DEG, DEL, and DEM were validated. This study reveals the regulatory mechanism of a candidate ceRNA network, providing insights into the potential mechanism of T. rubripes’ infection with C. irritans.

Despite significant advances in the development and refinement of immunotherapies administered to combat cancer over the past decades, a number of barriers continue to limit their efficacy. One significant clinical barrier is the inability to mount initial immune responses towards the tumor. As dendritic cells are central initiators of immune responses in the body, the elucidation of mechanisms that can be therapeutically leveraged to enhance their functions to drive anti-tumor immune responses is urgently needed. Here, we report that the dietary sugar L-fucose can be used to enhance the immunostimulatory activity of dendritic cells (DCs). L-fucose polarizes immature myeloid cells towards specific DC subsets, specifically cDC1 and moDC subsets. In vitro, L-fucose treatment enhances antigen uptake and processing of DCs. Furthermore, our data suggests that L-fucose-treated DCs increase stimulation of T cell populations. Consistent with our functional assays, single-cell RNA sequencing of intratumoral DCs from melanoma- and breast tumor-bearing mice confirmed transcriptional regulation and antigen processing as pathways that are significantly altered by dietary L-fucose. Together, this study provides the first evidence of the ability of L-fucose to bolster DC functionality and provides rational to further investigate how L-fucose can be used to leverage DC function in order to enhance current immunotherapy.

This study is a single-arm, single-center phase IV clinical trial on a rabies vaccine that has been marketed in China. The Vero cells and CTN-1V strain are used in the rabies vaccine product. The purpose of this study was to investigate the safety, immunogenicity and immune persistence of this product. One hundred and forty-nine participants were enrolled to the study, all of whom were included in the safety analysis set (SS), among which 116 participants were included in the protocol analysis set (PPS), One hundred and fifteen participants were included in the 6-month immune persistence analysis set (IPS6) and 111 in the 12-month immune persistence analysis set IPS12. Results showed that: 1) In the SS analysis set, adverse reactions were mainly pyrexia and pain at the vaccination site, the severity of which were mostly grade 1, and concentrated in 0–3 days after vaccination. No grade 3 or above adverse events and serious adverse events (SAE) related to the experimental vaccine were observed. 2) In the PPS analysis set, the antibody positive conversion rate reached 100% at 14 days after full immunization of the pre-immunized negative population; The antibody geometric mean titer (GMT) (95% CI) was 14.82 (13.00, 16.90). 3) The positive rate of serum neutralizing antibody was 93.91 % and the GMT at 1.58 IU/ml at 6 months after full immunization. The positive rate of neutralizing antibody was 85.59 % and GMT at 1.30 IU/ml at 12 months after immunization. Our results show that the human rabies vaccine with the CTN-1V strain and Vero cells as matrix had good safety, immunogenicity and immune persistence in our study.

Abstract Background Patients with non‐small‐cell lung cancer (NSCLC) and uncommon EGFR alterations typically have worse treatment outcomes than patients with classically EGFR‐mutated NSCLC. This study aimed to investigate the efficacy and safety of PD‐1 blockade with sintilimab plus anti‐angiogenic treatment with anlotinib in patients with NSCLC harboring uncommon EGFR mutations. Methods Patients with metastatic NSCLC harboring uncommon EGFR mutations after two previous treatments, including a platinum‐based chemotherapy regimen and a targeted treatment (or chemotherapy only for patients harboring EGFR ex20ins), received sintilimab combined with anlotinib. The primary endpoint was objective response rate (ORR). Results At data cutoff (September 27, 2022), median follow‐up was 22.3 months (range, 1.2–37.6). Among 21 enrolled patients, 12 had EGFR ex20ins and nine had other uncommon EGFR mutations such as L861Q, G719A, and G709X. Overall, eight patients (38.1%) achieved an objective response, and 18 (85.7%) achieved disease control. Median (95% CI) progression‐free survival (PFS) was 7.0 (5.4–8.6) months, and median overall survival (OS) was 20.0 (15.6–24.4) months. The 12‐month PFS rate (95% CI) was 22.2% (7.4–42.0), and the 12‐month OS rate was 66.7% (42.5–82.5). Patients harboring EGFR ex20ins had similar ORR and PFS to those with other mutations. Six patients (28.6%) experienced grade 3 treatment‐related adverse events (TRAEs); hand‐foot syndrome was the most common grade 3 TRAE (2 patients; 9.5%). No grade ≥4 TRAEs were observed. Conclusions The combination of sintilimab and anlotinib demonstrated durable efficacy and was generally well tolerated in patients with NSCLC and uncommon EGFR mutations who had received prior standard‐of‐care treatments. (ClinicalTrials.gov identifier: NCT04790409).

Abstract Gene therapy via retroviral vectors holds great promise for treating a variety of serious diseases. It requires the use of additives to boost infectivity. Amyloid-like peptide nanofibers (PNFs) were shown to efficiently enhance retroviral gene transfer. However, the underlying mode of action of these peptides remains largely unknown. Data-mining is an efficient method to systematically study structure–function relationship and unveil patterns in a database. This data-mining study elucidates the multi-scale structure–property–activity relationship of transduction enhancing peptides for retroviral gene transfer. In contrast to previous reports, we find that not the amyloid fibrils themselves, but rather µm-sized β-sheet rich aggregates enhance infectivity. Specifically, microscopic aggregation of β-sheet rich amyloid structures with a hydrophobic surface pattern and positive surface charge are identified as key material properties. We validate the reliability of the amphiphilic sequence pattern and the general applicability of the key properties by rationally creating new active sequences and identifying short amyloidal peptides from various pathogenic and functional origin. Data-mining—even for small datasets—enables the development of new efficient retroviral transduction enhancers and provides important insights into the diverse bioactivity of the functional material class of amyloids.

Accumulating evidence suggests that the gut microbiota plays an important role in the pathogenesis of inflammatory bowel disease (IBD). Carnosic acid (CA) is a major antioxidant component of rosemary and sage. Herein, we investigated the protective effects of dietary CA on dextran sodium sulfate (DSS)-induced colitis mouse model with an emphasis on its impact on the composition and metabolic function of gut microbiota. We found that CA effectively attenuated DSS-stimulated colitis in mice, as evidenced by reduced disease activity index (DAI), and systemic and colonic inflammation. Additionally, CA restored microbial diversity and improved the composition of gut microbiota in DSS-treated mice. Moreover, Spearman’s correlation coefficient showed a significant correlation between the fecal metabolites and the gut microbiota species. Changes in gut microbiota and the correlated metabolites might partially explain CA’s anti-inflammatory effects against colitis. Future clinical trials are needed to determine the therapeutic effects and mechanisms of CA on IBD in humans.

In this study, a multi-sensitive ion-imprinted polymer that serves as a highly selective absorption material for ruthenium (Ru(III)) in complicated solutions was designed and prepared with the adoption of Pickering High Internal Phase Emulsions (HIPEs) polymerization technology. Meawhile, acrylamide (AM) and acrylic acid (AA) were used as functional monomers, Ru(III) as template ion, ethylene glycol dimethacrylate (EGDMA) as cross-linking agent and the redox system ammonium persulfate-N,N,N′,N′-tetramethylethylenediamine (AP-TEMED) as initiator for the synthesis of a smart ruthenium ion-imprinted polymer (Ru(III)–SIIP). The chemical structure, morphology and magnetic properties of Ru(III)–SIIP were characterized and subsequently used for the selective adsorption of Ru(III). The results revealed that Ru(III)–SIIP had obvious temperature sensitivity/pH sensitivity/magnetic sensitivity. The maximum adsorption capacity of Ru(III) was 0.191 mmol/g and coupled with a desorption ratio of 82.99%. The screening of the adsorption kinetics of Ru(III)–SIIP indicated that the zero-order and pseudo-first-order kinetic mixed model was more suitable for describing the adsorption process, while the Langmuir model was suitable for describing the isotherm of Ru(III)–SIIP. Furthermore, an adsorption method combined with inductively coupled plasma atomic emission spectrometry (ICP-AES) based on Ru(III)–SIIP was established for Ru(III) and successfully applied in the detection of Ru(III) in mixed solutions. To conclude, Ru(III)–SIIP has broad prospects for the recovery of ruthenium in complex environmental situations.

The development of microbial communities is important for the growth of the fat greenling Hexagrammos otakii; however, the relationship between microbial communities and fish diet is poorly understood. Here, we used metagenomics sequencing to investigate the gut microbiota of H. otakii at three key time points during development. The gut microbial diversity and community composition of H. otakii presented stage-specific signatures and appeared to shift with different diets and environmental conditions such as NH4 + -NO2- etc. Metagenomics analysis indicated that the dominant phyla were Proteobacteria and Firmicutes. With dietary changes from rotifers and Artemia to formulated feed, the dominant genera shifted from Vibrio and Photobacterium to Lactococcus, and variations in the gut microbiota increased with age. Based on metagenomics functional annotation using the Kyoto Encyclopedia of Genes and Genomes database, growth and diet at different stages affected the metabolic function of the gut microbiome by activating carbohydrate and amino acid metabolism while weakening lipid and nucleotide metabolism. In addition, as predicted by the Carbohydrate-Active enZymes database, glycoside hydrolase and glycosyl transferases may be involved in food degradation. Our results suggest that the H. otakii gut microbiota assembly was coupled to animal development and host age-associated biotic features and changes. Diet had a considerable effect on these distinct communities at different times, indicating that the fish gut microbiota rapidly adapted to dietary shifts. The microbiota therefore likely plays an indispensable role in nutrient turnover and fermentation. These findings can provide guidance for the development of probiotics and the application of feed additives.

Abstract Background Massively parallel sequencing includes many liquid handling steps which introduce the possibility of sample swaps, mixing, and duplication. The unique profile of inherited variants in human genomes allows for comparison of sample identity using sequence data. A comparison of all samples vs. each other (all vs. all) provides both identification of mismatched samples and the possibility of resolving swapped samples. However, all vs. all comparison complexity grows as the square of the number of samples, so efficiency becomes essential. Results We have developed a tool for fast all vs. all genotype comparison using low level bitwise operations built into the Perl programming language. Importantly, we have also developed a complete workflow allowing users to start with either raw FASTQ sequence files, aligned BAM files, or genotype VCF files and automatically generate comparison metrics and summary plots. The tool is freely available at https://github.com/teerjk/TimeAttackGenComp/ . Conclusions A fast and easy to use method for genotype comparison as described here is an important tool to ensure high quality and robust results in sequencing studies.

Abstract Background Few large‐scale studies have been published using real‐world data related to overall survival (OS) improvements in advanced epidermal growth factor receptor (EGFR)‐mutant lung cancer patients; therefore, little is known regarding the characteristics of patients who could benefit most from EGFR‐tyrosine kinase inhibitors (TKIs). Our study aimed to assess whether EGFR‐TKI treatment confers survival benefits among advanced non‐small‐cell lung cancer (NSCLC) patients harboring EGFR mutations in the Chinese population. Patients and Methods A total of 6451 advanced NSCLC patients were diagnosed between January 1, 2013 and June 30, 2019 in Zhejiang Cancer Hospital. Ultimately, 2864 patients with a confirmed EGFR mutation genotype were enrolled in our study. OS was measured from the time of diagnosis of advanced NSCLC until death or last follow‐up. Results Median follow‐up for OS of advanced EGFR‐mutant NSCLC patients was 28.33 months in our study. Patients who received EGFR‐TKIs demonstrated better survival compared to those without EGFR‐TKI treatment (mOS: 29.77 vs. 22.97 months, p

Plant protection drone spraying technology is widely used to prevent and control crop diseases and pests due to its advantages of being unaffected by crop growth patterns and terrain restrictions, high operational efficiency, and low labor requirements. The operational parameters of plant protection drones significantly impact the distribution of spray droplets, thereby affecting pesticide utilization. In this study, a field experiment was conducted to determine the working modes of two representative plant protection drones and an electric backpack sprayer as a control to explore the characteristics of droplet deposition with different spray volumes in the citrus canopy. The results showed that the spraying volume significantly affected the number of droplets and the spray coverage. The number of droplets and the spray coverage area on the leaf surface were significantly increased by increasing the spray volume from 60 L/ha to 120 L/ha in plant protection drones. Particularly for the DJI T30, the mid-lower canopy showed a spray coverage increase of 52.5%. The droplet density demonstrated the most significant variations in the lower inner canopy, ranging from 18.7 droplets/cm2 to 41.7 droplets/cm2 by XAG V40. From the deposition distribution on fruit trees, the plant protection drones exhibit good penetration ability, as the droplets can achieve a relatively even distribution in different canopy layers of citrus trees. The droplet distribution uniformity inside the canopy is similar for XAG V40 and DJI T30, with a variation coefficient of approximately 50%-100%. Compared to the plant protection drones, the knapsack electric sprayer is suitable for pest and disease control in the mid-lower canopy, but they face challenges of insufficient deposition capability in the upper canopy and overall poor spray uniformity. The distribution of deposition determined in this study provides data support for the selection of spraying agents for fruit trees by plant protection drones and for the control of different pests and diseases.

Background Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TILs) is a promising immunotherapeutic approach for patients with advanced solid tumors. While numerous advances have been made, the contribution of neoantigen-specific CD4+T cells within TIL infusion products remains underexplored and therefore offers a significant opportunity for progress.Methods We analyzed infused TIL products from metastatic melanoma patients previously treated with ACT for the presence of neoantigen-specific T cells. TILs were enriched on reactivity to neoantigen peptides derived and prioritized from patient sample-directed mutanome analysis. Enriched TILs were further investigated to establish the clonal neoantigen response with respect to function, transcriptomics, and persistence following ACT.Results We discovered that neoantigen-specific TIL clones were predominantly CD4+ T cells and were present in both therapeutic responders and non-responders. CD4+ TIL demonstrated an effector T cell response with cytotoxicity toward autologous tumor in a major histocompatibility complex class II-dependent manner. These results were validated by paired TCR and single cell RNA sequencing, which elucidated transcriptomic profiles distinct to neoantigen-specific CD4+ TIL.Conclusions Despite methods which often focus on CD8+T cells, our study supports the importance of prospective identification of neoantigen-specific CD4+ T cells within TIL products as they are a potent source of tumor-specific effectors. We further advocate for the inclusion of neoantigen-specific CD4+ TIL in future ACT protocols as a strategy to improve antitumor immunity.

Abstract Background To explore the efficacy and prognostic factors of different treatment modalities on anaplastic lymphoma kinase (ALK)+ non‐small cell lung cancer (NSCLC) patients with brain metastases (BMs). Methods A total of 86 patients were enrolled into the study. They were divided into two cohorts based on their history of treatment with ALK tyrosine kinase inhibitors (ALK‐TKIs) prior to the incidence of BMs. ALK‐TKI‐naïve patients with BMs were included in cohort 1 (n = 59); patients who developed BMs after ALK‐TKIs treatment were enrolled in cohort 2 (n = 27). Prognostic factors related with overall survival (OS) when treated with ALK‐TKIs were assessed in multivariable analysis. Results With a median follow‐up of 41.8 months, the median OS was 34.8 months. In cohort 1, the OS, intracranial progression‐free survival (iPFS), and progression‐free survival (PFS) were 38.7 months (95% CI: 23.3 to 54.1), 18.5 months (95% CI: 9.6 to 27.4), and 19.1 months (95% CI: 13.7 to 24.5), respectively. Significantly improved OS and iPFS were noted in those patients in which second‐generation ALK‐TKIs versus crizotinib were initiated (OS: not reached vs. 29.0 months, p = 0.040; iPFS: 22.8 vs. 11.9 months, p = 0.035). In cohort 2, patients who experienced BMs as a result of the treatment failure of ALK‐TKIs had a median OS of 27.1 months. Considerable duration of stable disease in patients with measurable BMs was observed (iPFS: 11.5 months, 95% CI: 4.4 to 18.6; PFS: 12.2 months, 95% CI: 3.2 to 21.1). Conclusion Second‐generation ALK‐TKIs further improved the duration of intracranial response and survival in ALK+ NSCLC patients with BMs in a real‐world setting. The potent intracranial efficacy of second‐generation ALK‐TKIs might generate the lowered urgency of local treatment.

Citric acid (CA)-crosslinked cotton fabrics show a yellowish appearance because CA forms C=C bonds during the heating process. The whiteness was improved by sodium hydrosulfite (Na2S2O4), which was confirmed by the Fourier transform infrared spectra. The computational calculations showed that Na2S2O4 is more effective than H2O2 when the system of CA-treated cotton is bleached. Based on the reaction mechanism of Na2S2O4 bleaching, the influences of Na2S2O4 concentration, bleaching temperature, bleaching time, bleaching pH on whiteness, and wrinkle recovery angle were investigated. The optional bleaching condition was 14% Na2S2O4 and sodium pyrophosphate (Na4P2O7), 70°C, and 40 minutes. The effect on the performance of fabrics bleached with Na2S2O4 was similar to the effect of non-formaldehyde crosslinker 1,2,3,4-butane tetracarboxylic acid (BTCA) and the widely used crosslinker dimethyloldihydroxyethyleneurea-treated cotton. CA-treated cotton bleached by Na2S2O4 showed a good persistence of bleaching effect.

Fatty liver hemorrhagic syndrome (FLHS) in laying hens is a nutritional metabolic disease commonly observed in high-yielding laying hens. Sodium butyrate (NaB) and ferroptosis were reported to contribute to the pathogenesis of fatty liver-related diseases. However, the underlying mechanism of NaB in FLHS and whether it mediates ferroptosis remains unclear. A chicken primary hepatocyte induced by free fatty acids (FFAs, keeping the ratio of sodium oleate and sodium palmitate concentrations at 2:1) was established, which received treatments with NaB, the ferroptosis inducer RAS-selective lethal 3 (RSL3), and the inhibitor ferrostatin-1 (Fer-1). As a result, NaB increased biochemical and lipid metabolism indices, and the antioxidant level, while inhibiting intracellular ROS accumulation and the activation of the ferroptosis signaling pathway, as evidenced by a reduction in intracellular iron concentration, upregulated GPX4 and xCT expression, and inhibited NCOA4 and ACSL4 expression. Furthermore, treatment with Fer-1 reinforced the protective effects of NaB, while RSL3 reversed it by blocking the ROS/GPX4/ferroptosis pathway, leading to the accumulation of lipid droplets and oxidative stress. Collectively, our findings demonstrated that NaB protects hepatocytes by regulating the ROS/GPX4-mediated ferroptosis pathway, providing a new strategy and target for the treatment of FLHS.

Abstract Background Determining the tissue of origin (TOO) is essential for managing cancer of unknown primary (CUP). In this study, we evaluated the concordance between genome profiling and DNA methylation analysis in determining TOO for lung-specific CUP and assessed their performance by comparing the clinical responses and survival outcomes of patients predicted with multiple primary or with metastatic cancer. Methods We started by retrospectively screening for CUP patients who presented with both intra- and extrathoracic tumors. Tumor samples from included patients were analyzed with targeted sequencing with a 520-gene panel and targeted bisulfite sequencing. TOO inferences were made in parallel via an algorithm using genome profiles and time interval between tumors and via machine learning-based classification of DNA methylation profiles. Results Four hundred patients were screened retrospectively. Excluding patients definitively diagnosed with conventional diagnostic work-up or without available samples, 16 CUP patients were included. Both molecular approaches alone enabled inference of clonality for all analyzed patients. Genome profile enabled TOO inference for 43.8% (7/16) patients, and the percentage rose to 68.8% (11/16) after considering inter-tumor time lag. On the other hand, DNA methylation analysis was conclusive for TOO prediction for 100% (14/14) patients with available samples. The two approaches gave 100% (9/9) concordant inferences regarding clonality and TOO identity. Moreover, patients predicted with metastatic disease showed significantly shorter overall survival than those with multiple primary tumors. Conclusions Genome and DNA methylation profiling have shown promise as individual analysis for TOO identification. This study demonstrated the feasibility of incorporating the two methods and proposes an integrative scheme to facilitate diagnosing and treating lung-specific CUPs.

This paper designs an optimal open-loop leader-follower control strategy of input-delay stochastic systems. The leader-follower control problem is described as an optimal problem based on Stackelberg strategies. A control strategy of the leader is given to minimize the function of $H_{2}$ norm, while a control strategy of the follower in worst case maximizing the function of $H_\infty $ norm is applied to the systems. Then the optimal leader-follower control strategy is obtained by establishing the information relationship of the forward and the backward variables with augmentation of the variables and solving several Riccati equations. At last, an example illustrates the effectiveness of the proposed strategy.

IntroductionGut microbiota have been linked to modulating susceptibility to Type 1 diabetes; however, there are many ways in which the microbiota interact with host cells, including through microbial ligand binding to intracellular inflammasomes (large multi-subunit proteins) to initiate immune responses. NLRP6, a microbe-recognizing inflammasome protein, is highly expressed by intestinal epithelial cells and can alter susceptibility to cancer, obesity and Crohn’s disease; however, the role of NLRP6 in modulating susceptibility to autoimmune diabetes, was previously unknown.MethodsWe generated NLRP6-deficient Non-obese diabetic (NOD) mice to study the effect of NLRP6-deficiency on the immune cells and susceptibility to Type 1 diabetes development.ResultsNLRP6-deficient mice exhibited an expansion of CD103+ B cells and were protected from type 1 diabetes. Moreover, NLRP6-deficient CD103+ B cells express regulatory markers, secreted higher concentrations of IL-10 and TGFb1 cytokines and suppressed diabetogenic T cell proliferation, compared to NLRP6-sufficient CD103+ B cells. Microarray analysis of NLRP6-sufficient and -deficient CD103+ B cells identified 79 significantly different genes including genes regulated by lipopolysaccharide (LPS), tretinoin, IL-10 and TGFb, which was confirmed in vitro following LPS stimulation. Furthermore, microbiota from NLRP6-deficient mice induced CD103+ B cells in colonized NLRP6-sufficient germ-free mice; however, the long-term maintenance of the CD103+ B cells required the absence of NLRP6 in the hosts, or continued exposure to microbiota from NLRP6-deficient mice.DiscussionTogether, our data indicate that NLRP6 deficiency promotes expansion and maintenance of a novel TGF -dependent CD103+ Breg population. Thus, targeting NLRP6 therapeutically may prove clinically useful.

The phenotypic efficacy of somatic copy number alterations (SCNAs) stems from their incidence per base pair of the genome, which is orders of magnitudes greater than that of point mutations. One mitotic event stands out in its potential to significantly change a cell's SCNA burden-a chromosome missegregation. A stochastic model of chromosome mis-segregations has been previously developed to describe the evolution of SCNAs of a single chromosome type. Building upon this work, we derive a general deterministic framework for modeling missegregations of multiple chromosome types. The framework offers flexibility to model intra-tumor heterogeneity in the SCNAs of all chromosomes, as well as in missegregation- and turnover rates. The model can be used to test how selection acts upon coexisting karyotypes over hundreds of generations. We use the model to calculate missegregation-induced population extinction (MIE) curves, that separate viable from non-viable populations as a function of their turnover- and missegregation rates. Turnover- and missegregation rates estimated from scRNA-seq data are then compared to theoretical predictions. We find convergence of theoretical and empirical results in both the location of MIE curves and the necessary conditions for MIE. When a dependency of missegregation rate on karyotype is introduced, karyotypes associated with low missegregation rates act as a stabilizing refuge, rendering MIE impossible unless turnover rates are exceedingly high. Intra-tumor heterogeneity, including heterogeneity in missegregation rates, increases as tumors progress, rendering MIE unlikely.

Abstract Background Brain metastasis is a common and lethal complication of non-small cell lung cancer (NSCLC). It is mostly diagnosed only after symptoms develop, at which point very few treatment options are available. Therefore, patients who have an increased risk of developing brain metastasis need to be identified early. Our study aimed to identify genomic and epigenomic biomarkers for predicting brain metastasis risk in NSCLC patients. Methods Paired primary lung tumor tissues and either brain metastatic tissues or cerebrospinal fluid (CSF) samples were collected from 29 patients with treatment-naïve advanced NSCLC with central nervous system (CNS) metastases. A control group comprising 31 patients with advanced NSCLC who died without ever developing CNS metastasis was also included. Somatic mutations and DNA methylation levels were examined through capture-based targeted sequencing with a 520-gene panel and targeted bisulfite sequencing with an 80,672 CpG panel. Results Compared to primary lung lesions, brain metastatic tissues harbored numerous unique copy number variations. The tumor mutational burden was comparable between brain metastatic tissue (P = 0.168)/CSF (P = 0.445) and their paired primary lung tumor samples. Kelch-like ECH-associated protein (KEAP1) mutations were detected in primary lung tumor and brain metastatic tissue samples of patients with brain metastasis. KEAP1 mutation rate was significantly higher in patients with brain metastasis than those without (P = 0.031). DNA methylation analysis revealed 15 differentially methylated blocks between primary lung tumors of patients with and without CNS metastasis. A brain metastasis risk prediction model based on these 15 differentially methylated blocks had an area under the curve of 0.94, with 87.1% sensitivity and 82.8% specificity. Conclusions Our analyses revealed 15 differentially methylated blocks in primary lung tumor tissues, which can differentiate patients with and without CNS metastasis. These differentially methylated blocks may serve as predictive biomarkers for the risk of developing CNS metastasis in NSCLC. Additional larger studies are needed to validate the predictive value of these markers.

Abstract Background There is only limited knowledge of the treatment responses and clinical outcomes of immune checkpoint inhibitors (ICIs) in driver gene‐negative non‐small cell lung cancer (NSCLC) patients with brain metastases (BM). This study aims to assess the efficacy of immunotherapy in these patients in a real world setting. Methods NSCLC‐BM patients without driver gene mutations who received ICIs were retrospectively identified between July 2017 and December 2019. The primary observation endpoint was intracranial objective response rate (iORR), and secondary objectives were objective response rate (ORR), intracranial and systemic progression‐free survival (iPFS, PFS), and overall survival (OS). Results We reviewed 1578 patients with lung cancer and BM. According to the exclusion criteria, 41 patients were finally enrolled. Among these 41 patients, iORR was 36.6% (95% confidence interval [CI] = 21.2%–52.0%), whereas iPFS was 6.8 (95% CI = 3.32–10.35) months. Additionally, ORR, PFS, and OS were 24.4% (95% CI = 10.7%–38.1%), 6.2 (95% CI = 4.57–7.83) months and 13.7 (95% CI = 11.20–16.26) months, respectively. ICIs combined with concurrent radiotherapy group exhibited preferred iORR (p = 0.030) compared with no radiotherapy group, and ICIs plus chemotherapy showed improved OS (p = 0.024) compared to ICI monotherapy. Moreover, the lines of ICI treatment ≥2 (p = 0.005) and derived neutrophil‐to‐lymphocyte ratio (dNLR) ≥3 (p = 0.010) were independently negative factors for OS. Conclusion In NSCLC‐BMs patients lacking driver genes, ICIs exhibited an effective drug regime. A combination of ICIs with concurrent radiotherapy showed a better intracranial response, whereas ICIs plus chemotherapy were associated with superior OS.

Summary: Understanding the heterogenicity of tumor-infiltraing lymphocyte (TIL) populations and the immunobiology in human cancer is a key to establish efficient immunotherapies. Here, we have established a protocol for the characterization of CD8+ TILs in tumors by single-cell RNA-seq paired to VDJ profiling and chromatin structure including dissociation of tumor biopsies. We have also provided guidance for subsequent fluorescence-activated cell sorting (FACS), single-cell encapsulation, bioinformatics analysis, and troubleshooting.For complete details on the use and execution of this protocol, please refer to Anadon et al. (2022). : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Colon cancer (CC) is a common malignant tumor worldwide, and ferroptosis plays a vital role in the pathology and progression of CC. Effective prognostic tools are required to guide clinical decision-making in CC. In our study, gene expression and clinical data of CC were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We identified the differentially expressed ferroptosis-related lncRNAs using the differential expression and gene co-expression analysis. Then, univariate and multivariate Cox regression analyses were used to identify the effective ferroptosis-related lncRNAs for constructing the prognostic model for CC. Gene set enrichment analysis (GSEA) was conducted to explore the functional enrichment analysis. CIBERSORT and single-sample GSEA were performed to investigate the association between our model and the immune microenvironment. Finally, three ferroptosis-related lncRNAs (XXbac-B476C20.9, TP73-AS1, and SNHG15) were identified to construct the prognostic model. The results of the validation showed that our model was effective in predicting the prognosis of CC patients, which also was an independent prognostic factor for CC. The GSEA analysis showed that several ferroptosis-related pathways were significantly enriched in the low-risk group. Immune infiltration analysis suggested that the level of immune cell infiltration was significantly higher in the high-risk group than that in the low-risk group. In summary, we established a prognostic model based on the ferroptosis-related lncRNAs, which could provide clinical guidance for future laboratory and clinical research on CC.

Deep ocean regeneration of dissolved silica (DSi) is an essential part of the ocean silica cycle and is driven by a complex series of biogeochemical processes. Here we compare the distributions of DSi and other environmental parameters in several western Pacific marginal seas to explore the role of marginal seas in deep ocean DSi regeneration. Results show that in oligotrophic marginal seas (such as the South China Sea), the DSi content in deep waters is similar to that of the adjacent Pacific waters. However, in productive marginal seas (such as the Bering Sea), the DSi content in deep waters is markedly higher than that in adjacent Pacific waters at the same depths. This is mainly due to deep ocean DSi regeneration in the marginal sea basin, which is fueled by the high biogenic particle flux from the productive surface waters. On a global scale, deep ocean DSi regeneration is accelerated in productive marginal seas, causing marginal seas such as the Bering Sea to have the highest DSi concentrations of all global waters.

Objective: To assess the immunogenicity and safety of the enterovirus 71 vaccine (Vero cell) (EV71 vaccine) and trivalent split-virion influenza vaccine (IIV3). Methods: Healthy infants aged 6–7 months were recruited from Zhejiang Province, Henan Province, and Guizhou Province and randomly assigned to the simultaneous vaccination group, EV71 group, and IIV3 group at a ratio of 1:1:1. Then, 3 mL blood samples were collected before vaccination and 28 days after the second dose of vaccine. Cytopathic effect inhibition assay was used to detect EV71 neutralization antibody, and cytopathic effect inhibition assay was used to detect influenza virus antibody. Results: A total of 378 infants were enrolled and received the first dose of vaccine and were included in the safety analysis, and 350 infants were involved in the immunogenicity analysis. The adverse events rates were 31.75%, 28.57%, and 34.13% in the simultaneous vaccination group, EV71 group, and IIV3 group (p > 0.05), respectively. No vaccine-related serious adverse events were reported. After two doses of EV71 vaccine, the seroconversion rates of EV71 neutralizing antibody were 98.26% and 97.37% in the simultaneous vaccination group and the EV71 group, respectively. After two doses of IIV3, the simultaneous vaccination group and the IIV3 group, respectively, had seroconversion rates of 80.00% and 86.78% for H1N1 antibody, 99.13% and 98.35% for H3N2 antibody, and 76.52% and 80.99% for B antibody. There was no statistically significant difference in the seroconversion rates of influenza virus antibodies between groups (p > 0.05). Conclusions: The coadministration of EV71 vaccine and IIV3 has good safety and immunogenicity in infants aged 6–7 months.

The use of drones in agriculture is expanding at a brisk pace in crop production due to the superiority in precision, efficiency, and safety of their applicators. However, their potential drift risk also raises concern for users and regulatory authorities. The method of wind tunnel research can effectively evaluate the weighted influence of each drift factor, especially the drift characteristics of the nozzle and spray solution. Based on the wind tunnel test results, centrifugal nozzles have a higher drift risk than hydraulic nozzles, even with a similar DV50. The cumulative drift rate of the centrifugal nozzle at 2 m downwind was 90.1% compared to the LU12001 nozzle’s 40.6% under the wind speed of 3.5 m/s. Compared with the same coding as the flat fan hydraulic nozzle, the IDK nozzle can effectively reduce the drift rate. For the tested nozzles, DV50 and wind speed had a linear relationship with drift rate, and the sampling location had an exponential or logarithmic relationship with drift rate. Spray adjuvants, especially modified vegetable oils, had a significant effect on reducing the amount of drift. The results of this experiment provide a reference for the selection of nozzles and the addition of spray adjuvants. Further clarifying the spray drift characteristics of drones until a drift prediction model is available is still the focus of research.

Cell type classification is an important problem in cancer research, especially with the advent of single cell technologies. Correctly identifying cells within the tumor microenvironment can provide oncologists with a snapshot of how a patient’s immune system reacts to the tumor. Wide and deep learning (WDL) is an approach to construct a cell-classification prediction model that can learn patterns within high-dimensional data (deep) and ensure that biologically relevant features (wide) remain in the final model. In this paper, we demonstrate that regularization can prevent overfitting and adding a wide component to a neural network can result in a model with better predictive performance. In particular, we observed that a combination of dropout and ℓ2 regularization can lead to a validation loss function that does not depend on the number of training iterations and does not experience a significant decrease in prediction accuracy compared to models with ℓ1, dropout, or no regularization. Additionally, we show WDL can have superior classification accuracy when the training and testing of a model are completed data on that arise from the same cancer type but different platforms. More specifically, WDL compared to traditional deep learning models can substantially increase the overall cell type prediction accuracy (36.5 to 86.9%) and T cell subtypes (CD4: 2.4 to 59.1%, and CD8: 19.5 to 96.1%) when the models were trained using melanoma data obtained from the 10X platform and tested on basal cell carcinoma data obtained using SMART-seq. WDL obtains higher accuracy when compared to state-of-the-art cell classification algorithms CHETAH (70.36%) and SingleR (70.59%).

Clubroot is a devastating disease that causes substantial yield loss worldwide. However, the inheritance and molecular mechanisms of clubroot resistance during pathogen infection in radish remain largely unclear. In this study, we investigated the inheritance of clubroot resistance in the F2 population derived from crossing clubroot-resistant (CR) and clubroot-susceptible inbred lines “GLX” and “XNQ,” respectively. Genetic analysis revealed that a single dominant gene controlled the clubroot resistance of “GLX” with a Mendelian ratio of resistance and susceptibility of nearly 3:1. Bulked segregant analysis combined with whole-genome resequencing (BSA-seq) was performed to detect the target region of RsCr6 on chromosome Rs8. Linkage analysis revealed that the RsCr6 locus was located between two markers, HB321 and HB331, with an interval of approximately 92 kb. Based on the outcomes of transcriptome analysis, in the RsCr6 locus, the R120263140 and R120263070 genes with a possible relation to clubroot resistance were considered candidate genes. In addition, three core breeding materials containing the two reported quantitative trait loci (QTLs) and our novel locus RsCr6 targeting clubroot resistance were obtained using marker-assisted selection (MAS) technology. This study reveals a novel locus responsible for clubroot resistance in radishes. Further analysis of new genes may reveal the molecular mechanisms underlying the clubroot resistance of plants and provide a theoretical basis for radish resistance breeding.

Vibrational energy transfer in water involves intermolecular coupling of O-H stretching modes, but much less is known about the role of the bending modes. Here the authors, combining static and femtosecond infrared, Raman, and hyper-Raman spectroscopy and ab initio molecular dynamics simulations, provide insight into the energy dynamics of the bend vibrations.

Brain metastasis (BM) is a common complication in non-small cell lung cancer (NSCLC), which associates with poor prognosis. Recently, immune checkpoint inhibitors (ICIs) has revolutionized the treatment of tumors. Programmed death-1 (PD-1)/programmed death ligand 1 (PD-L1) inhibitors could produce antitumor effect by activating the autoimmune system. The immunotherapy has already show to have a promising outcome for NSCLC patients with BM, while its specific curative effect and the most ideal mode of the treatment remain to be explored. Here we reviewed the tumor microenvironment (TME) in BM lesions and summarized the role of PD-1/PD-L1 inhibitors in cerebral and its current status in clinical studies.

Abstract Plant phenotyping under field conditions plays an important role in agricultural research. Efficient and accurate high‐throughput phenotyping strategies enable a better connection between genotype and phenotype. Unmanned aerial vehicle‐based high‐throughput phenotyping platforms (UAV‐HTPPs) provide novel opportunities for large‐scale proximal measurement of plant traits with high efficiency, high resolution, and low cost. The objective of this study was to use time series normalized difference vegetation index (NDVI) extracted from UAV‐based multispectral imagery to characterize its pattern across development and conduct genetic dissection of NDVI in a large maize population. The time series NDVI data from the multispectral sensor were obtained at five time points across the growing season for 1,752 diverse maize accessions with a UAV‐HTPP. Cluster analysis of the acquired measurements classified 1,752 maize accessions into two groups with distinct NDVI developmental trends. To capture the dynamics underlying these static observations, penalized‐splines (P‐splines) model was used to obtain genotype‐specific curve parameters. Genome‐wide association study (GWAS) using static NDVI values and curve parameters as phenotypic traits detected signals significantly associated with the traits. Additionally, GWAS using the projected NDVI values from the P‐splines models revealed the dynamic change of genetic effects, indicating the role of gene–environment interplay in controlling NDVI across the growing season. Our results demonstrated the utility of ultra‐high spatial resolution multispectral imagery, as that acquired using a UAV‐based remote sensing, for genetic dissection of NDVI.

The post-assessment of highway atmospheric environmental impacts was limited by the traditional air pollution prediction model, which cannot adapt to complex terrain and complex obstacle scenes. The traditional model has a single evaluation index, which cannot accurately evaluate and predict the transient and long-term emissions of various pollutants. Based on the computational fluid dynamics model, this work establishes a post-assessment method of the atmospheric environment impact of the Beijing–Chengde Expressway construction project. The main pollution factors NOx and CO of highway traffic for transmission and diffusion simulation analysis were selected. The influence law of traffic function, environmental impact, meteorological conditions, and landform on the diffusion of pollution factors in complex tunnel sections were analyzed. It concludes that the pollution within 200 m along the expressway is severe and mainly concentrated in the tunnel entrance and gully area. The NOx concentration is generally higher than CO. The environmental quality is not up to standard and has a diffusion trend with increased traffic flow, operation time, wind speed, wind temperature, and wind direction frequency. The research results can provide theoretical guidance and technical support for the scientific post-assessment of highway environmental impact under complex conditions.

Herein, the microstructure and mechanical properties of hydrogels consisting of unrinsed sturgeon surimi (URSS) and plant-derived polysaccharides such as κ-carrageenan (KC), konjac gum (KG), xanthan gum (XG), guar gum (GG) and sodium alginate (SA), were studied by texture analysis, rheological measurement and scanning electron microscopy (SEM). Rheological results showed that the apparent viscosity, storage modulus (G′) and loss modulus (G″) of URSS increased by addition of KC, KG, GG and SA. The gel strength of resultant surimi products fabricated with KG/URSS mixture was significantly higher than that of other groups. KG could significantly improve the hardness (44.14 ± 1.14 N), chewiness (160.34 ± 8.33 mJ) and cohesiveness (0.56 ± 0.02) of the unrinsed surimi gel. Adding SA and KC had no significant effect on the textural characteristics of printed gels. However, an apparent decrease in the relevant mechanical properties of printed hydrogels was observed when XG and GG were added into surimi. SEM indicated that the incorporation of KG and KC could further integrate the gel structure of URSS as compared to hindering the cross-linking of surimi protein by XG and GG, which were in accordance with gel strength and water-holding capacity. These results provided useful information to regulate the 3D printing performance in functionalized surimi-based material.

Abstract Background Advances in medical technology have allowed for customized prognosis, diagnosis, and treatment regimens that utilize multiple heterogeneous data sources. Multiple kernel learning (MKL) is well suited for the integration of multiple high throughput data sources. MKL remains to be under-utilized by genomic researchers partly due to the lack of unified guidelines for its use, and benchmark genomic datasets. Results We provide three implementations of MKL in R. These methods are applied to simulated data to illustrate that MKL can select appropriate models. We also apply MKL to combine clinical information with miRNA gene expression data of ovarian cancer study into a single analysis. Lastly, we show that MKL can identify gene sets that are known to play a role in the prognostic prediction of 15 cancer types using gene expression data from The Cancer Genome Atlas, as well as, identify new gene sets for the future research. Conclusion Multiple kernel learning coupled with modern optimization techniques provides a promising learning tool for building predictive models based on multi-source genomic data. MKL also provides an automated scheme for kernel prioritization and parameter tuning. The methods used in the paper are implemented as an R package called RMKL package, which is freely available for download through CRAN at https://CRAN.R-project.org/package=RMKL.

Abstract Background Long non-coding RNA (lncRNA) expression data have been increasingly used in finding diagnostic and prognostic biomarkers in cancer studies. Existing differential analysis tools for RNA sequencing do not effectively accommodate low abundant genes, as commonly observed in lncRNAs. Results We investigated the statistical distribution of normalized counts for low expression genes in lncRNAs and mRNAs, and proposed a new tool lncDIFF based on the underlying distribution pattern to detect differentially expressed (DE) lncRNAs. lncDIFF adopts the generalized linear model with zero-inflated Exponential quasi-likelihood to estimate group effect on normalized counts, and employs the likelihood ratio test to detect differential expressed genes. The proposed method and tool are applicable to data processed with standard RNA-Seq preprocessing and normalization pipelines. Simulation results showed that lncDIFF was able to detect DE genes with more power and lower false discovery rate regardless of the data pattern, compared to DESeq2, edgeR, limma, zinbwave, DEsingle, and ShrinkBayes. In the analysis of a head and neck squamous cell carcinomas data, lncDIFF also appeared to have higher sensitivity in identifying novel lncRNA genes with relatively large fold change and prognostic value. Conclusions lncDIFF is a powerful differential analysis tool for low abundance non-coding RNA expression data. This method is compatible with various existing RNA-Seq quantification and normalization tools. lncDIFF is implemented in an R package available at https://github.com/qianli10000/lncDIFF.

Abstract Background The rapid development of single-cell RNA sequencing (scRNA-seq) provides unprecedented opportunities to study the tumor ecosystem that involves a heterogeneous mixture of cell types. However, the majority of previous and current studies related to translational and molecular oncology have only focused on the bulk tumor and there is a wealth of gene expression data accumulated with matched clinical outcomes. Results In this paper, we introduce a scheme for characterizing cell compositions from bulk tumor gene expression by integrating signatures learned from scRNA-seq data. We derived the reference expression matrix to each cell type based on cell subpopulations identified in head and neck cancer dataset. Our results suggest that scRNA-Seq-derived reference matrix outperforms the existing gene panel and reference matrix with respect to distinguishing immune cell subtypes. Conclusions Findings and resources created from this study enable future and secondary analysis of tumor RNA mixtures in head and neck cancer for a more accurate cellular deconvolution, and can facilitate the profiling of the immune infiltration in other solid tumors due to the expression homogeneity observed in immune cells.

This study explores the interpersonal space (IPS) and peripersonal space (PPS) of Chinese people and evaluates the relationship between the two spaces for different directions and genders. Seventy-one participants were recruited for this study. Participants were required to determine their IPS in eight directions (0°, 45°, 90°, 135°, 180°, 225°, 270°, 315°) when approached by male or female confederates in the comfort distance task. Each participant was also asked to judge their PPS in five directions (0°, 45°, 90°, 270°, 315°) following the same procedure. Results showed that their IPS was significantly influenced by direction (p < 0.05), with the largest distance in the front (0°) and the closest distance in the rear (135°, 180°, 225°), indicating non-circular IPS among Chinese subjects. Moreover, the PPS on the right side (90°) was larger than in other directions (0°, 45°, 270°, 315°). Participants maintained larger IPS than PPS in the front, but the IPS was closer than PPS on the right and left sides. When facing a female confederate, larger IPS was preferred than PPS, whereas the opposite held true when facing a male confederate. Comparison of participants’ arm length and PPS showed that the reachability distance was overestimated in the front but underestimated laterally. The findings of this study can be applied to environmental design, space utilization, and social interaction.

The introduction of tyrosine kinase inhibitors (TKI) has transformed chronic myeloid leukemia (CML) into a chronic disease with long‐term survival exceeding 85%. However, resistance of CML stem cells to TKI may contribute to the 50% relapse rate observed after TKI discontinuation in molecular remission. We previously described a model of resistance to imatinib mesylate (IM), in which K562 cells cultured in high concentrations of imatinib mesylate showed reduced Bcr‐Abl1 protein and activity levels while maintaining proliferative potential. Using quantitative phosphoproteomic analysis of these IM‐resistant cells, we have now identified significant upregulation of tumor progression locus (Tpl2), also known as cancer Osaka thyroid (COT1) kinase or Map3k8. Overexpression of Tpl2 in IM‐resistant cells was accompanied by elevated activities of Src family kinases (SFKs) and NF‐κB, MEK‐ERK signaling. CD34+ cells isolated from the bone marrow of patients with CML and exposed to IMin vitro showed increased MAP3K8 transcript levels. Dasatinib (SFK inhibitor), U0126 (MEK inhibitor), and PS‐1145 (IκB kinase (IKK) inhibitor) used in combination resulted in elimination of 65% of IM‐resistant cells and reduction in the colony‐forming capacity of CML CD34+ cells in methylcellulose assays by 80%. In addition, CML CD34+ cells cultured with the combination of inhibitors showed reduced MAP3K8 transcript levels. Overall, our data indicate that elevated Tpl2 protein and transcript levels are associated with resistance to IM and that combined inhibition of SFK, MEK, and NF‐κB signaling attenuates the survival of IM‐resistant CML cells and CML CD34+ cells. Therefore, combination of SFK, MEK, and NF‐κB inhibitors may offer a new therapeutic approach to overcome TKI resistance in CML patients.

Vector-borne diseases are responsible for > 1 million deaths every year but genomic resources for most species responsible for their transmission are limited. This is true for neglected diseases such as sleeping sickness (Human African Trypanosomiasis), a disease caused by Trypanosoma parasites vectored by several species of tseste flies within the genus Glossina. We describe an integrative approach that identifies statistical associations between trypanosome infection status of Glossina fuscipes fuscipes (Gff) flies from Uganda, for which functional studies are complicated because the species cannot be easily maintained in laboratory colonies, and ∼73,000 polymorphic sites distributed across the genome. Then, we identify candidate genes involved in Gff trypanosome susceptibility by taking advantage of genomic resources from a closely related species, G. morsitans morsitans (Gmm). We compiled a comprehensive transcript library from 72 published and unpublished RNAseq experiments of trypanosome-infected and uninfected Gmm flies, and improved the current Gmm transcriptome assembly. This new assembly was then used to enhance the functional annotations on the Gff genome. As a consequence, we identified 56 candidate genes in the vicinity of the 18 regions associated with Trypanosoma infection status in Gff. Twenty-nine of these genes were differentially expressed (DE) among parasite-infected and uninfected Gmm, suggesting that their orthologs in Gff may correlate with disease transmission. These genes were involved in DNA regulation, neurophysiological functions, and immune responses. We highlight the power of integrating population and functional genomics from related species to enhance our understanding of the genetic basis of physiological traits, particularly in nonmodel organisms.

With the breakthroughs achieved of programmed death-1 (PD-1)/PD-L1 inhibitors monotherapy as first-line and second-line treatment in advanced non-small cell lung cancer (NSCLC), the treatment strategy is gradually evolving and optimizing. Immune combination therapy expands the benefit population and improves the curative effect. A series of randomized phase III trials are ongoing. In this review, we discuss the prospect and current situation of immune checkpoint inhibitors in first-line treatment in advanced NSCLC patients.